Does anyone know of an algorithm that can perform automated gating of different bead populations used for multiplexed flow cytometry assays? As you can see from the attached dot plot there are almost 40 subpopulations which would need to be identified. I know that there are a number of different automated gating algorithms but I wouldn't like to test all of them. I have tried kmeans clustering in Matlab (both with the fluorescence intensities and with the log-intensities), but it doesn't work. Any useful insight would be greatly appreciated.

Peter